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Yorodumi- PDB-5c7q: Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c7q | ||||||
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Title | Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase | ||||||
Components | NudF protein | ||||||
Keywords | HYDROLASE / Nudix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.52 Å | ||||||
Authors | Gabelli, S.B. / de la Pena, A.H. / Suarez, A. / Amzel, L.M. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. Authors: de la Pena, A.H. / Suarez, A. / Duong-Ly, K.C. / Schoeffield, A.J. / Pizarro-Dupuy, M.A. / Zarr, M. / Pineiro, S.A. / Amzel, L.M. / Gabelli, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c7q.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c7q.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 5c7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/5c7q ftp://data.pdbj.org/pub/pdb/validation_reports/c7/5c7q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21291.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: nudF, Bd3179 / Plasmid: pET24 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6MIH8, ADP-ribose diphosphatase |
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-Non-polymers , 6 types, 370 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.75-2.0 M ammonium sulfate, 0.1 M HEPES pH 7.0, and 0-0.5% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.948 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 22, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→50 Å / Num. obs: 58801 / % possible obs: 94.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.111 / Χ2: 1.702 / Net I/av σ(I): 23.897 / Net I/σ(I): 6.6 / Num. measured all: 362440 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2062 / WRfactor Rwork: 0.1753 / FOM work R set: 0.8153 / SU B: 1.742 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0852 / SU Rfree: 0.0852 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.76 Å2 / Biso mean: 23.001 Å2 / Biso min: 11.37 Å2
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Refinement step | Cycle: final / Resolution: 1.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.522→1.561 Å / Total num. of bins used: 20
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